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#include <iostream>

#include "SimilarityTMAlign.h"
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using namespace std;
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int main(int argc, char** argv) {

  String* locationDB;
  String* filenameList;
  String* locationOut;
  String* filenameOut;
  String* locationTMAlign;

  if (argc < 6) {
    cout << "Error in the input arguments. The execution must be: " << endl;
    cout << "./ComputeMatrixTMAlign <Location TM-Aling> <Location PDB Files> <File with PDB List> <Output Folder> <Common Name Outfile>" << endl;
    return 0;
  }
  else {
    cout << "---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------" << endl;
    cout << "      Location TM-Align : " << argv[1] << endl;
    cout << "     Location PDB Files : " << argv[2] << endl;
    cout << "     File with PDB List : " << argv[3] << endl;
    cout << "          Output Folder : " << argv[4] << endl;
    cout << "    Common Name Outfile : " << argv[5] << endl;
    cout << "---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------" << endl;
    locationTMAlign = new String(argv[1]);
    locationDB      = new String(argv[2]);
    filenameList    = new String(argv[3]);
    locationOut     = new String(argv[4]);
    filenameOut     = new String(argv[5]);
  }

  SimilarityTMAlign* similarityTMAlign = new SimilarityTMAlign();

  similarityTMAlign->LocationTMAlign(locationTMAlign);
  similarityTMAlign->LocationDB(locationDB);
  similarityTMAlign->FilenameList(filenameList);
  similarityTMAlign->LocationOut(locationOut);
  similarityTMAlign->FilenameOut(filenameOut);
  similarityTMAlign->GetSimilarityData();

  cout << "---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------" << endl;

  if (similarityTMAlign) delete similarityTMAlign;

  return 1;

}
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